|
| Status |
Public on Sep 21, 2021 |
| Title |
HCT116 DKO1 Nanopore-Seq |
| Sample type |
SRA |
| |
|
| Source name |
colorectal cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HCT116
|
| Growth protocol |
Cell lines were cultured in McCoy’s 5A modified medium (Gibco, #16600-082) supplemented with heat inactivated foetal bovine serum (10%, Gibco, 16000-044).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
HCT116 and DKO1 DNA (1 μg) was sheared using the Covaris g-TUBE spun at 3400 x g in 2 x 60 sec spins.
Sheared DNA was prepared for Nanopore sequencing using the Ligation 1D kit (SQK-LSK109) according to manufacturer’s instructions. Each cell line was sequenced on one PromethION flow cell.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
PromethION |
| |
|
| Data processing |
Reads were base called with Guppy v3.3.0 on a GPU-enabled Sun Grid Engine high performance computing server (parameters “--chunks_per_runner 1500 --gpu_runners_per_device 1 --cpu_threads_per_caller 4 -x "cuda:0 cuda:1 cuda:2 cuda:3" -r” and configuration “dna_r9.4.1_450bps_hac_prom.cfg”).
Base called reads (fastq) were aligned to hg19 using minimap2 (Li 2018) (v.2.17-r943-dirty) with parameters “-ax map-ont”. Mapped reads were sorted and indexed with SAMtools (v1.9).
Variants were called and phased with medaka_variant (v0.11.4, https://nanoporetech.github.io/medaka) with the options “-t 36 -s r941_prom_high_g330 -m r941_prom_high_g330 -p -b 100”.
Genome_build: GRCh37/hg19
|
| |
|
| Submission date |
Oct 20, 2020 |
| Last update date |
Sep 22, 2021 |
| Contact name |
Qian Du |
| E-mail(s) |
q.du@garvan.org.au
|
| Organization name |
Garvan Institute of Medical Research
|
| Street address |
384 Victoria St
|
| City |
Darlinghurst |
| State/province |
NSW |
| ZIP/Postal code |
2010 |
| Country |
Australia |
| |
|
| Platform ID |
GPL26167 |
| Series (2) |
| GSE158011 |
DNA methylation maintains integrity of higher order genome architecture |
| GSE159663 |
DNA methylation maintains integrity of higher order genome architecture (Nanopore) |
|
| Relations |
| BioSample |
SAMN16484258 |
| SRA |
SRX9317106 |
